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conservative/radical nonsynonymous distances method in Bio::Align::DNAStatistics #16

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Albert Vilella (Albert Vilella) Original Redmine Issue: 2142, https://redmine.open-bio.org/issues/2142 Original Date: 2006-11-13 Original Assignee: Bioperl Guts

As in:

http://www.bio.psu.edu/People/Faculty/Nei/Lab/hon-new2.htm

As I see it, we already have most of what we need in Bio::Align::DNAStatistics.

Need to add 3 hashes for the polar, charge, and Miyata Yasunaga divisions of the 20 AAs.

The add a method, very similar to the dnds “counting” method we already have, to count the changes.

We can add the differences and standard errors calculation, and then we will have everything needed to produce the 3 matrices as in the example OUTFILE of the hon-new2 implementation.

All this is for a given Ts/Tv ratio, the method for which we already have.

This method only makes sense for CDS sequences, so an extra check should be added.

cjfields commented 7 years ago

@avilella still interested in this?